Comparing the Prognostic Value of BAP1 Mutation Pattern, Chromosome 3 Status, and BAP1 Immunohistochemistry in Uveal Melanoma

Abstract

Uveal melanoma (UM), a tumor of the eye, can be divided into 2 major classes correlating with patients' prognosis. Gene expression profiles and chromosome 3 status are correlated with tumor classification and prognosis. Somatic BAP1 mutations are another feature largely restricted to metastatic UM. Here we performed thorough BAP1 mutation analysis including sequencing and gene dosage analysis of all BAP1 coding exons as well as methylation analysis of the promoter CpG island in a set of 66 UMs. The results were compared with the BAP1 protein expression as determined by immunohistochemistry and the tumor-related survival of the patients. BAP1 sequencing and gene dosage analysis of BAP1 exons by multiplex ligation-dependent probe amplification revealed a mutation in 33 (89%) of 37 tumors with monosomy 3 (M3) or isodisomy 3. BAP1 mutations were not detected in any of the 28 tumors with disomy 3 or partial monosomy 3 (partM3). Most of the sequence mutations (21 of 28) were frame-shift, splice-site, or nonsense mutations leading to a premature termination codon. BAP1 protein as determined by immunohistochemistry was absent in all samples with a BAP1 mutation irrespective of the functional type of mutation. Kaplan-Meier analysis revealed a highly significant association between BAP1 protein staining and patients' survival (P=0.0004). The association between BAP1 mutation status and tumor-related survival was less pronounced but still significant (P=0.0023). We conclude that BAP1 protein staining is favorable over BAP1 mutation screening by Sanger sequencing for prognostic testing of UM patients.

Patterns of BAP1 protein expression provide insights into prognostic significance and the biology of uveal melanoma

“…In the current study, this included tumours resected because of size, location, recurrence, secondary complications, and patient preference. Whilst we recognize that there may be a potential bias as compared with an analysis of all UM, the frequency of nBAP1 negativity in this study (54%) is consistent with that reported in the literature (43–58%) 23, 38, 39. Similar to these other reports, we demonstrated a correlation between loss of nBAP1 expression and poor prognostic parameters known to be associated with ‘high risk’ UM – i.e.…”

“…For example, Van de Nes et al demonstrated in a cohort of 66 UM that 33/37 (89%) M3 UM had a BAP1 mutation together with an absence of nBAP1 protein expression 23. A similar proportion was reported by Koopmans et al in their study of 74 UM, with 88% of the M3 UM harbouring a BAP1 mutation together with loss of nuclear protein expression 39.…”

“…More recently, mutations occurring in UM have been identified in several genes, including GNAQ , GNA11 , BAP1 , SF3B1 , EIF1AX , PLCB4 , and CYSLTR2 11, 18, 19, 20, 21, 22. In particular, inactivating BAP1 mutations are associated with a poor outcome, being present in ∼84% of all UMs that went on to produce metastases 19, 23, 24. BAP1 mutations similarly correspond with a significantly worse prognosis in renal clear cell carcinoma 25 and cholangiocarcinoma 26, whilst in mesothelioma BAP1 inactivation is associated with a good prognosis 27.…”

“…Functionally, BAP1 nonsense or frameshift mutations lead to truncated BAP1 protein with loss of nuclear localisation and/or reduced protein or mRNA stability 23. This has led to several recent studies assessing the prevalence of nuclear BAP1 protein expression (nBAP1) in UM, and correlating this with clinical outcome 23, 38, 39.…”

“…This has led to several recent studies assessing the prevalence of nuclear BAP1 protein expression (nBAP1) in UM, and correlating this with clinical outcome 23, 38, 39. Koopmans et al 39 and Kalirai et al 38 observed loss of nBAP1 protein expression in 43% and 51% of all UM, respectively, which was significantly associated with increased metastatic risk, along with other clinical features linked to poor prognosis.…”